The Talk
by All-Aboard-the-Nathan-James
Summary: They've been putting this off for a long time. Tom and Rachel have each been dealing with their own demons and their arguments with each other, & it's time they talked. This started as a 2x13 fix-it fic, describing the way I think the finale scene between Tom and Rachel should have gone. Now it's a continuation of their story & how I wish things had played out for them in season 3.
1. The Talk

Rachel handed him the envelope and Tom took it, trying not to be so aware of the way her hand briefly brushed his. He looked down at the envelope, and then back up at her. She looked uncertain, as if she wasn't really sure what to say. She dropped her hand, pausing for a moment, and then looked like she was about to say something, so Tom said, "Can we talk?"

Rachel looked at him in confusion for a moment, and then nodded. Tom managed a brief, reassuring smile and nodded his head toward his door in invitation. Rachel nodded again, looking away. Tom opened the door, and held it open, motioning for her to go in first. She met his eyes briefly, nervously, and then headed into the room.

Rachel walked in, and turned around to face him as Tom pulled the door quietly closed behind them. Rachel watched as he sat his hat gently down on the desk. She was all too aware of the fact that she was alone with Thomas Chandler in his hotel room, and reminded herself to breathe. She was pretty sure her heart was beating so loudly he could hear it across the room.

 _What is wrong with you?_ She thought to herself. _Get a hold of yourself._

Her inner turmoil was interrupted when Tom turned to her and asked, "Are we okay?"

The question was so unexpected that Rachel found herself unable to answer. For a moment, she just stared at him, her mouth slightly ajar, and then she looked away.

Tom seemed to take this as a bad sign. He sighed, then, taking a step toward her, said, "please just talk to me."

When remembering the conversation later, Rachel wasn't quite sure what had set her off. Perhaps it was the tension in the room. Perhaps it was his plea for honesty. Perhaps it was the fact that she was leaving the next morning, and felt that now she could finally tell him the truth. Most likely, it was that everything they had been through together had been leading up to this moment, and on some level Rachel knew what needed to be said.

"No," she said quietly. "We're not okay."

Tom wanted to protest this, but something in Rachel's expression told him that this time, he needed to hear her out. She crossed her arms over her chest defensively, and glanced up at him, clearly expecting him to argue with her. When he said nothing, she broke eye contact and started pacing. He had noticed she did that a lot when she was nervous, worried or confused.

"Nothing is okay," she began. "Everything is different. We're on land now, and I'm leaving in the morning." As she paced, she didn't notice how Tom's face fell at the reminder of her imminent departure. "You have a job to do here, and I have a job to do elsewhere, and… Well, things are not okay between us. They haven't been, since…"

"I know," Tom said, interrupting her for the first time.

She looked back at him, her arms still crossed, and studied his face. He didn't look angry. If anything, he looked pained. Rachel could feel a small bit of hope rise in her chest. Perhaps this situation was gnawing at him the same way it was her. The longer they went without talking about what had happened, the more Rachel felt it eating away at her. She took a deep breath, and continued.

"We don't talk anymore," she said, resuming her pacing. "Not like we used to." She paused, studying her feet. After a moment, she looked up at him again. "I told you I would always be straight with you. And I wasn't. For that, I am sorry." She paused, just long enough to judge his reaction, but not long enough for him to say anything before rushing on. "What I did… I did what I felt needed to be done. I… I didn't think about the problems it would cause for you. I only let myself think about my job. My mission. Find the cure. Save the world." At that, she laughed mirthlessly, and shook her head. "Killing Neils was the only way I was going to get what I needed. And, in my mind, it was fair." She expected Tom to say something here, but he just continued to stare blankly at her, with his frustratingly blank expression that was impossible to read. That expression always drove her mad.

"I wanted justice, Tom." She sighed, then finally stopped pacing, and took a step closer to Tom, looking him in the eyes. "Look," she said. "I am not going to lie to you. I wanted Neils dead. I wanted him to get what he deserved, and I knew there is no infrastructure left in the world to bring justice. I wanted to save people. Neils knew that his lungs were the key to the airborne cure, and he played me Tom. He knew I needed his help, so he wouldn't give it." She shook her head, looking away again, pausing. Then she shrugged. "I guess it's not use trying to justify what I did. I just wanted you to know why I did it. I… I never meant to change things between us. I didn't want to ruin our… friendship. I only wanted to do what I thought was right."

Rachel paused for a while, and Tom figured she was finished. Slowly, he uncrossed his arms, dropping them to his side with a sigh. "I'm sorry, too," he said quietly.

Rachel looked up at him sharply, a look of surprise on her face. Meeting her eyes, Tom could tell she was hoping she understood him, but was trying to keep herself from hoping too much. Tom supposed that was the most she could bring herself to open up to disappointment.

"I should have talked to you," he continued. "I was angry. I was confused. I thought… I thought we understood each other, until then. I felt…" Tom didn't want to say it. _Betrayed._ How could he feel betrayed? Rachel wasn't one of his crew. Before the mission, they had been total strangers. She owed no real allegiance to him, save for being on his ship. So, when she had killed Neils, why did he feel betrayed?

Inside, Tom knew the answer. He had felt betrayed because he had thought they were friends. Confidants, even. They had been through so much together, survived the end of the world together. And even though they fought frequently, he had thought they had understood each other. They were both on a mission, one he had thought they shared, until the end.

After a moment, Tom realized he had been silent too long. He wasn't sure what to say, so he just said the first things that came to his mind. "I should have talked to you. Not just after, but before. I should have made sure we were on the same page, instead of focusing so much on the Ramseys. You're right, we used to talk. Until I started pushing you away. I wish I hadn't, Rachel."

Rachel felt her heart skip a beat. She felt heat rising to her cheeks, and tried unsuccessfully to control her breathing. She wasn't sure why, but hearing him use her first name always made her feel things she had been suppressing for months. Things she hadn't been willing to even admit she was feeling, even to herself.

Rachel looked down at the floor and muttered, "We pushed each other away, Tom."

He nodded, but she didn't see it. After a long pause, he asked, "Why?"

Slowly Rachel forced herself to look at him again. "Why what?"

"Why did we push each other away?" he asked, looking at her intently, his expression still unreadable.

Rachel shrugged, and shook her head. She couldn't bring herself to admit why she had pushed him away. She settled for a half-truth. "Because we couldn't let anything get in the way of the mission."

Tom nodded again. "But the mission is over," he said simply.

Rachel waited for him to say more, but he didn't, so she just said, "I suppose."

"So can we talk again?" Tom asked.

Rachel sighed, and nodded, a small smile finally finding its way to her lips.

Tom waited to see if Rachel would say anything, and when she didn't, he figured it was his turn for honesty. "I suppose I pushed you away because I didn't know what to do with you, Dr. Scott," he said, matching Rachel's small smile, a hint of humor in his voice. Rachel met his eyes again, her smile growing slowly. He continued. "You were the most frustrating person I ever met. The only one who challenged me, who questioned me. In you I found someone who was as driven as I was, as passionate as I was, and smarter than anyone I know. I guess that's why we butted heads to often," he chuckled slightly.

Rachel, unable to control her breathing yet again, was fairly sure she was blushing profusely. That awareness only made the blush more. She attempted a weak chuckle as well. "We're too much alike for our own good," she laughed nervously.

Tom, for his part, was completely calm, finally feeling like he knew what he wanted. "We are," he said, "And that confused me, at first." Tom knew he had pushed her away, at least in part, because he wasn't willing to face his growing feelings for her. Well, now he was. "But that doesn't have to be a bad thing," he offered.

Rachel grinned. "I suppose not," she managed.

Tom went on. "I pushed you away because you were unlike anyone I've ever met, and I didn't know what to do. The truth is, Rachel, you fascinated me. If I got too close, I was afraid I'd lose myself in you, and…"

"And you were afraid that getting too close would jeopardize the mission," Rachel finished for him. Tom nodded, dumbfounded. "I… I suppose I did the same thing," she finished lamely.

They just stared at each other for a minute, the tension growing, until Rachel, attempting to diffuse the situation, laughed, "I told you, too much alike."

To her surprise, Tom kissed her. At first she was shocked, but after a moment, she decided it was time to let down her defenses. Slowly, she began to kiss him back. She felt him put his hands on her hips, pulling her closer, and she rested her hands on his chest, deepening the kiss slightly.

After a minute, Tom pulled back, leaving them both breathless. He kept his forehead on hers, and as Rachel slowly opened her eyes, she saw that his were still closed. She didn't want to ruin the moment, but she couldn't lose sight of her job, either.

"Tom," she whispered, causing him to open his eyes and smile at her. "I still have to leave in the morning."

Tom's smile fell, and Rachel momentarily wished she hadn't said anything. She'd ruined the moment. But she knew it was what she had to do. Her work was her life, and she knew Tom would understand that. They were, after all, very much alike. He wouldn't ask her to change.

"I know," he whispered, pulling his head back and looking her in the eyes. "I just couldn't let you leave without knowing everything was okay between us."

Rachel smiled at him, giving him the first full, genuine smile she had smiled in months. "We're okay," she said, and leaned in to kiss him again quickly. Reluctantly, she pulled back, extricating herself from his embrace. "I'm going to go now," she said. "Thanks for the talk."

He smiled and nodded, then moved out of her way so she could get to the door. Rachel walked to the door, wishing she could just stay here, lost in this moment forever, but knowing she would never forgive herself if she neglected her job. There were still people out there who needed her, and she wouldn't fail them.

Tom watched as she made her way to the door, and was relieved when she put her hand on the doorknob but turned around to look at him one last time. "Be safe," he said, his face returning to an unreadable mask. Rachel now knew that meant he was hiding emotions he didn't want her to see. For the first time, she was glad he hid his emotions. She didn't know if she would have been able to resist it if he had asked her to stay. She met his eyes one last time, and he said, "When you get back, find me."

Rachel intended to do just that.


	2. Vigil

**A/N: So this fic originally started as a one-shot, but I felt it deserved some more story to it.** **So this chapter picks up after Rachel's shooting, while she is still unconscious in the hospital. Hope you guys like this chapter, and let me know if it's worth continuing! Thanks for reading!**

Tom sat at Rachel's bedside in the cold, bleak hospital room. He was leaning against the rail of the bed, watching Rachel as she laid there. She looked so pale, and it made Tom's heart hurt to see her like that.

 _She'd probably be embarrassed for all of us to see her like this_ , he thought. She had always worked so hard to look strong, hiding her weaknesses deep where no one could see them. Tom smiled to himself as he thought about all the times they had bickered on the ship, both of them hiding their feelings behind walls and clashing constantly.

In the last 24 hours, Tom had played over every one of their arguments in his mind. Now that he knew what he wanted, it was clear to him how much his feelings for her had gotten in the way of their work together. The more he had tried to hide them, not even admitting them to himself, the more he had sidelined her. As his feelings grew, they had argued more and more, and Tom suddenly wished he could have those days back. He wished he could go back and change all of the times he had been harsh to her. He wished he could have been honest with her from the start, but that had been impossible for him for so many reasons.

Now he wished he could tell her how sorry he was for all of that. But now it may be too late. Tom hoped he hadn't waited too long.

"God, Rachel," Tom whispered to her sleeping form. "I'm so sorry." He buried his face in his hands, his elbows still resting on the bar of the hospital bed.

Just then, to Tom's slight annoyance, there was a soft knock on the door. Tom rubbed his face and sighed, sitting back in his chair and said, "Come in."

He stood up and saluted when President Michener came in the room. "At ease, Commander," Michener said, and Tom dropped his hand, giving the President a curt nod.

Tom, who had been lost in his thoughts just a moment before, searched for something to say, but before he came up with anything Michener held out his hand. He held a small white envelope out to Tom and said, "I believe this was meant for you." Tom took it with a questioning look, and Michener continued, "it was in the envelope with the epidemiological models you gave me from Dr. Scott," he said with a respectful nod toward the bed behind them. "I believe she meant for you to get it before giving the rest to me. Figured I would bring it by."

"Thank you, sir," Tom said, turning the envelope over in his hands. He saw his name written on the front side of the envelope and recognized Rachel's small, scribbled handwriting. In spite of himself, the sight brought a small smile to Tom's lips.

"Well," Michener said, bringing Tom's attention back to the moment. "I have a meeting to get to, so I'll leave you to it." As he said it, he noticed Tom's attention drift back down to the envelope in his hand. "Commander," Michener said, softer this time. "When was the last time you ate?" Michener knew Tom hadn't left Rachel's bedside since the doctors had said she was stable and let him in.

"I'll be fine, sir," Tom said respectfully.

Michener suppressed a smile. Chandler never made it easy. "All the same, I'll send someone by with some food in a little," he said.

Tom started to say that wasn't necessary, but he knew better than to argue with the new President, so he simply nodded. Michener left the room, and Tom sat back down in the chair and studied the envelope in his hand.

He had briefly wondered why Rachel had given the epidemiological models to him if they had been meant for the President, but in the confusion after the shooting he hadn't thought anything of it and had simply given the President the envelope without opening it. Apparently Rachel had meant for him to open it first. He looked up toward the bed and smiled, wondering what she would say if she were awake.

 _When you know I'm on the verge of leaving, I give you a mysterious envelope, and you don't even open it_ , he imagined her admonishing him with a laugh and a shake of her head. Of course, he would have told her that she had said it was for the President, so he had passed it along as told.

Tom chuckled to himself, then returned to the yet unopened envelope in his hand. He turned it over to the back side and opened it carefully, attempting not to rip the envelope or whatever was inside.

He pulled out a folded piece of paper and unfolded it slowly. At the top it was formally addressed to Commander Thomas Chandler. Lower, Rachel has begun the note with just his first name: _Tom,_

Tom skimmed the letter, but his eyes caught on the last, small paragraph:

 _Goodbye for now, Captain. It has been a pleasure working with you. I hope our paths cross again in the future._

 _Love,_

 _Rachel Scott_

Clearly this letter was her goodbye letter to him before she left for the trip the President had ordered her on. Tom shook his head, and folded the note back up, placing it carefully back inside the envelope.

"Thank you for the letter, Rachel," he said quietly to where Rachel laid on the bed. "But I'm not going to read this right now." He paused, before adding, "This isn't goodbye. This isn't the end for us. It can't be." Tom sighed, placing the envelope on the end table next to him and leaning on the rails of the bed once more. For some reason, he couldn't bring himself to read the goodbye letter she had written to him. Not while she laid in that hospital bed, fighting an unconscious fight for her life. Reading the letter seemed too final. It made it seem like she was leaving. And Tom couldn't bear the thought of her leaving, not now. Not after everything they'd been through.

"You're going to pull through," Tom whispered. "You have to. You're too stubborn not to," he said, smiling sadly to himself. "There are still people out there who need you, Doctor. Just because we found the cure doesn't mean your work is over. You're too important to the world." Tom paused, then added quietly, "And too important to me."

Tom rested his chin on his hands and looked at Rachel's face, forcing himself to keep it together. He did his best to fight the emotions welling inside him, but a few tears escaped nonetheless. "I can't lose you too," he said, letting the words fall away into the silent room. "We've lost too many people already. We lost Quincy, and then Walker, Chung, and Bivas… I lost Darien, and I won't lose you too..." Tom trailed off, wiping his face, partially glad Rachel wasn't awake to see him like this. He needed her to be strong and pull through, so he needed to be strong for her.

Tom leaned back in his chair once more, his eyes never leaving Rachel's face. The doctor should be back to give him an update sometime soon, and Tom prayed it would be a good one. He silently promised Rachel he would not leave the room until she woke up.


	3. Awakenings and Explanations

When Rachel woke up, she found herself in an unfamiliar hospital room, surrounded by dim lights and a soft beeping sound. Rachel opened her eyes slowly, her head feeling foggy. She blinked a few times, trying to get her bearings. Realizing she was in a hospital bed, she had a brief moment of confusion. She tried to sit up, but a sharp pain in her shoulder made her lay back down with a wince, and she was reminded of the events just previous to her loss of consciousness.

Rachel squeezed her eyes shut again, trying to banish the memories from her head. She was becoming increasingly aware of the pain in her shoulder. She noticed that her arm was wrapped in a sling. With her good hand, she tried to move the sling slightly so she could see the wound in her shoulder and assess its severity, but the movement jarred her shoulder and she gasped in pain, wincing again.

Just then, Rachel heard a rustling sound coming from the left side of the bed, and she forgot about the sling and turned her attention toward the sound. To her surprise, she found Tom occupying the room's lone chair. He appeared to have been asleep. She must have woken him.

For a moment, Rachel wasn't sure what he was doing there, and then she remembered the conversation they had shared in his hotel room the previous night. At least she hoped it had been the previous night; she wasn't sure how long she had been out. She laid back in her bed, not moving, watching as Tom woke up, rubbing his eyes and blinking. She waited as he tried to discern where the noise that had woken him had come from, and smiled as he checked the machines and then turned his attention to her.

Rachel grinned at the surprised look that took over Tom's face when his eyes met hers and he saw that she was awake. "Hello, Captain," she said quietly, then coughed, her voice still scratchy with disuse.

Tom blinked a few more times, still partially asleep, before answering, "You're awake."

"Perceptive as ever," she responded lightheartedly, and Tom smiled.

"Well," Tom said, matching her lighthearted tone, "I was going to ask how you are feeling, but if you're well enough to tease me I'd say you're feeling better."

Rachel laughed, but the movement jarred her shoulder again and she fought back another wince. She coughed again, both to cover her wince and clear her voice. "What are you doing here?" She asked.

Tom gave her an incredulous look. "Do you really have to ask me that?" he said.

"Yes," Rachel responded simply, then waited for him to answer.

Tom sighed. "I was making sure you were okay. And," he said, moving closer and taking Rachel's good hand in both of his, "I wanted to be here for you when you woke up."

For a moment, Rachel was dumbfounded. The last thing she had expected was to wake up to Tom sitting vigil by her bedside. She had always known Tom to be fiercely loyal and determined, but she had never been the subject of those traits before. To know that he had sat there for God knows how long just watching over her meant more to her than she could say, and she had to fight back tears. This embarrassed her, so she pretended like it was nothing, and attempted to cover up her emotions with a weak attempt at humor. "Well, I'm awake now, Captain," she said teasingly, "You are released from your duty as my lifeguard."

Tom just smiled. "I'm not leaving," he said, giving her no room to argue the point further.

Rachel knew ordering him from the room was pointless, and besides, she didn't particularly want him to leave. "Well," she sighed, "If you're going to stay here, you might as well make yourself useful. Would you sit this bed up, please?" Tom nodded, dropped her hand with another smile, and went to do as told. It took him a minute or so to find the right button, but he found it and pressed it until the bed raised itself up into a sitting position.

When the bed was as upright as it would get, Tom took the railing off the side of the bed and sat down next to Rachel, taking her hand in his again. After a moment of silence, Tom met Rachel's eyes, and she asked, "What happened?"

Tom sighed, trying to decide where to start and how much to tell her. "What's the last thing you remember?" he asked.

Rachel forced herself to think back to that night, as much as she would just like to forget it ever happened. "When I got to my hotel room, there was a man there. He… He asked me if I was the one who created the cure…" She trailed off, and Tom noticed she had a faraway, glassy look in her eyes. He squeezed her hand slightly, and she looked back at him. "I don't know," she said quietly. "He said a few other things, but it's all kind of a blur now…"

"It's alright," Tom said. "That's fine. The man was a rogue immune, one of Ramsey's men who wasn't on the sub with them," he informed her.

"How… How do you know that?" She asked, hoping she knew the answer but not sure.

"We caught him, Rach," Tom said, and smiled when Rachel breathed a sigh of relief and closed her eyes. Tom continued, "I heard the shot, and so did Tex. I sent him to get Doc Rios, and then to secure the building. I stayed with you. We made sure that whoever had done this wasn't going to get out. We got him."

Rachel opened her eyes again and whispered, "Thank you." Tom just gave her hand another squeeze.

Rachel's gaze shifted from Tom's face to the door behind him, and Tom turned as the door opened and the doctor came in. He stood up from the bed, placing Rachel's hand back at her side, and moved back to the corner of the room to get out of the doctor's way.

"Well, it looks like someone is feeling better," the doctor said, and Rachel smiled slightly and nodded. It was a very businesslike smile, and Tom could tell she was slightly annoyed at the doctor's interruption. "It's good to have you back, Dr. Scott," he said,

"It's good to be back," Rachel said. "So, when can I get out of here?"

The doctor just laughed, and Rachel gave him the same polite but slightly annoyed smile again. "All in good time Doctor, you know that." Rachel sighed, and Tom had to hold back a laugh at the look of exasperation on her face. At least she seemed to be taking this well.

The doctor did a few more routine checks, changed the bandages on Rachel's shoulder, and left them with the information that she was healing nicely and should be able to leave soon. When they were alone in the room once more, tom returned to his seat on the edge of Rachel's bed, and she leaned back on the bed with a heavy sigh.

"I hate being confined to hospital beds," she complained, and Tom briefly wondered if she had been confined to one in the past. He made a note to ask her that later, realizing that, for how well they had gotten to know each other, he knew almost nothing about her past. He felt like the Rachel before the one that had shown up on his ship was a complete stranger. "I feel so useless here," Rachel added.

Tom smiled, although she didn't see it because her eyes were closed again. "You're allowed to be useless for a few more days," Tom joked. "You've earned it." Although Rachel didn't open her eyes, the corners of her mouth turned up in a smile. "Just give it a few more days, and you'll be out there bossing people around again in no time," he added with a chuckle.

Rachel opened her eyes this time and looked over at him with a smile. She seemed to notice something, and glanced toward the side table next to Tom's chair with a frown. "That's… my letter," she said, not sure what to make of its presence there. Tom had forgotten he had left it sitting on the table. He picked it up again, and Rachel asked, "did… did you read it?" When Tom shook his head, she said, "I think you should. It explains a lot."

Tom nodded at her. "Alright," he said, and began taking the letter out of the envelope.

"Not right now!" Rachel exclaimed, her face growing red. "Read it later."

Tom grinned. "Whatever you say, doctor," he laughed, and Rachel laid back down again, closing her eyes with a sigh.

Rachel's smile waned a little, and Tom could tell she was fading. "I'm tired again," she whispered.

"Go back to sleep, Rach," Tom said quietly, and Rachel's breathing got slower again.

Tom watched her for a while, and when he was sure she was asleep, Tom removed the letter from the envelope again and read it in its entirety this time.

 _Tom,_

 _If you are reading this, you probably already know that I will be leaving in the morning. The President has sent me to investigate reports of fresh outbreaks of the virus, and I don't know when I will return. I was going to say goodbye to you in person, but to be honest I couldn't bring myself to tell you I am leaving. So here we are._

 _I wanted to say thank you for everything you have done for me, Captain Chandler. I know I haven't been easy to work with throughout this mission, but you have been there for me every step of the way. You challenged me when I got stuck, and believed in me when I was ready to give up on myself. You stood up for me in front of your crew, and risked everything for a mission simply because I asked you to. For that, I am truly grateful._

 _I suppose I am writing this because I want us to part ways as friends. The President has included me in his pardon, but his isn't the forgiveness I need. I hope someday I will see you again and we can talk this all over in person, but I wanted to say I am sorry for causing such a rift between us. I believe what I did was justified, but I see now how much it put your mission in jeopardy and undermined you. I never meant to cause such problems, I only did what I had to in order to find the key to the airborne cure. I never meant to lose you as a friend in the process._

 _To help explain why I did what I did, let me tell you a story. When I was young, my parents took me with them on a mission trip to Africa. While we were there, my mother was infected with malaria. Although it was treatable, my father refused to allow her treatment, believing that God would save her if it were His will for her to live. She didn't make it. As soon as I was old enough to leave, I returned to England to study medicine. I vowed to save as many lives as I could. I never spoke to my father again._

 _When working with Niels, I was reminded of this. Niels knew that his genes held the key to the airborne cure, but he refused to work with me. He had already killed millions, and he knew how to make the cure airborne, but he refused. He refused to save the lives of countless people, because he thought he was some kind of god. Since he refused to work with me, I knew I could never make the cure airborne without killing him._

 _I don't regret it. I did what I had to do to save the rest of the world. I refused to let people die because of the stubborn beliefs of one man. All I regret is that my actions broke our friendship. I should have come to you about it. For that, I'm sorry._

 _I don't know why I'm telling you all of this. I guess I just hope that it helps you understand me a little, and that one day you can find it in your heart to forgive me. I wish I had the courage to say this in person, because I don't want our friendship to end like this._

 _I don't know what it is, this bond that we shared, but I hope I have not broken it beyond repair. Someday I will tell you all of this in person, as I owe you that much. But for now, I hope I leave you with the explanation you deserve. Anyway, I suppose I have talked long enough._

 _Goodbye for now, Captain. It has been a pleasure working with you. I hope our paths cross again in the future._

 _Love,_

 _Rachel Scott_

When he was finished reading, Tom dropped the letter to his lap, staring at the wall in front of him for a moment. In light of their conversation the previous evening, Tom wasn't sure what to make of her letter. He had long since forgiven Rachel for Niels' death, and now, after reading her explanation, he wished he hadn't been so harsh with her. He had been so angry at her for jeopardizing their leverage by killing Niels that he hadn't even thought about why she might have done it. He had treated her like a criminal, when all she was trying to do was the right thing. In their determination to push each other away, they had both alienated the other, and Tom figured he was just as responsible for Niels' death as she was.

He sat there watching Rachel as she slept, feeling as if he knew her a lot better now. "You're not the only one in need of forgiveness, Rachel," he whispered to the silent room.

He leaned over the edge of the bed and placed a gentle kiss on her forehead before resuming his previous place in the chair.

Despite what Rachel had said earlier, he would continue his vigil. He didn't ever want to be relieved of the duty of watching over her.


	4. Bedtime Story

Two days later, the doctor had cleared her, and Rachel was determined to get out of the hospital as quickly as she could. In her room's small bathroom, she struggled out of the hotel gown and into some of her clothes that Tom said he'd had Lt. Foster gather for her while she was out. She chose the loosest sweater in her pack, figuring it would be the easiest to get her arm into without ripping her stitches. While she was doing that, she had sent Tom on a mission to the front desk to take care of her clearing paperwork so she could get done faster.

When she had managed to get the sweater over her head with one hand and had given up the battle of taming her hair, Rachel returned to the main room and found Tom waiting by the door. "Is the paperwork in order?" she asked him.

Tom nodded. "Yes ma'am. You're good to go."

Rachel grinned. "Let's get out of here, then," she said, making her way toward his position by the door.

"Just one thing," Tom said when she was standing in front of him, waiting for him to vacate the doorway so she could leave. She looked up at him, her expression a mix of questioning annoyance. "Where are you going to go?"

That gave her pause. She hadn't considered that. It had been so long since she'd had to think about where to go. With a start, she realized that the Nathan James had become her home. When she had left on the mission, she had known she would likely never return to her true home, and so she had unwittingly adopted the ship as her home. Now that they were docked, she wasn't sure where she was supposed to go. Her face fell, and she dropped her gaze to the floor.

Tom saw her crestfallen look, and wished he could take back those words. The answer seemed pretty obvious to him. "Come back with me," he said. Rachel looked up at him, but said nothing, so he continued, "We've secured the hotel, and I'm still staying there. They moved me to the top floor, so I have a nice suite and an extra room. You're welcome to it, if you want it."

Rachel look uncertain, and opened her mouth a few times, but kept checking herself, as if she was unsure what to say. When she spoke, she was embarrassed to hear her voice shake lightly with nervousness. "I…. I don't think I can go back there," she said, averting her eyes again.

Tom was confused for a second, but when he saw the scared look she was trying to keep from her eyes, he understood. To tell the truth, he probably wouldn't be comfortable having her in that hotel again either. "That's alright," he said soothingly. "There's a hotel attached to this hospital. They're mostly housing refugees here, but I'm sure they have some rooms open. Why don't I see if they can get us a suite here instead?"

Rachel looked relieved, but said, "You don't have to come with me. I'll be fine on my own."

Tom shook his head. "I'm not leaving you alone again. So unless you want me to post more guards on you, I'm coming with you."

Rachel would never admit it, but having him close made her feel safer, and despite herself she was glad he insisted they stay together for the time being. "Fine," she sighed, and Tom smiled in triumph.

"You wait here," he said. "I'll go see if they have anything available."

Rachel nodded, and sat back down on the bed as Tom left to find someone to give them a room. He came back a few minutes later, and Rachel could tell by the look on his face that he'd had to do some ordering around to get what he wanted. She gave him an expectant look, and he sighed. "They don't have any suite rooms available in this hotel, but they're giving us adjoining rooms, so we'll have to make do with that."

"Alright," Rachel said, "good enough. Let's go, then."

* * *

Later that night, when Tom had moved his few possessions into his new hotel room, he sat on the couch in Rachel's room, her head on his shoulder as they watched a movie. It was an old one, but since none of the TV stations were working, they had to make do with the DVDs the hotel had on hand. He'd made them popcorn, and was relieved when Rachel ate it. It was the first thing he had gotten her to eat since leaving the hospital. When he had tried to make dinner, she had said everything reminded her of "hospital food" and refused to eat it. Thankfully the popcorn had won her over.

When the movie ended, it was nearly 22:00 hours, and Tom had caught Rachel yawning more than once. As the credits rolled, she sat up, removing her head from his shoulder, but said nothing.

"Well," Tom said, fighting back a yawn of his own, "I think it's time we both get some rest." He stood up, stretching, and Rachel frowned, still silent. She ran a hand absently through her hair, staring at the ground. Tom looked at her curiously, but began making his way to the door that connected into his room. "I'm going to go now," he said cautiously, but Rachel just nodded again. Confused, Tom headed to the door.

When he began to open it, Rachel finally stopped him, standing up from the couch and turning to face him. "Tom?" she asked, and he looked back to her, worry starting to show on his face. "Could you… Um… Could you not leave?" she asked quietly.

Tom closed the door and walked back over to where she stood in front of the couch. He looked at her for a moment, but she refused to meet his eyes, wariness evident on her face. After a few seconds of silence, he said, "What's wrong?"

Rachel attempted a shrug, but forgot she couldn't do so without pain, and silently cursed her shoulder. "It's just…" she tried, but she wasn't quite sure how to put her feelings into words.

She looked scared and worried, and Tom thought he knew what the problem was. With a reassuring smile, he reached over and brushed a strand of hair from her face, tucking it behind her ear before cupping her face in his hand. That got her to look up and finally meet his eyes again. "Rach," he said quietly, "We caught the guy. You're safe here."

Rachel was momentarily distracted by the warmth of his hand on her face, and for a few seconds she just stared into his eyes. It took her a few extra moments to process what he had said, and when she did, she felt her face grow red with embarrassment. She should be stronger than this. Her fears felt childish, but she couldn't help but feel them nonetheless.

"I know," she whispered. "It's just… Every time I close my eyes, I see his face," she confessed, her voice wavering slightly. "I can't sleep like this… I can't… I just don't want to be alone right now." she wanted to say more, but she was afraid she'd lose it, so she gave up.

Tom saw how close she was to crying, so he removed his hand from her face and wrapped it around her good shoulder, pulling her to his chest. She leaned into him, trying not to cry.

"I'll stay," he said, kissing the top of her head. "You're safe with me."

Tom moved around her and sat down on the couch, pulling her down beside him. She curled up next to him, and he pulled a blanket off the back of the couch and draped it over her. He reached up and turned off the lamp on the end table, plunging the room into darkness. He felt Rachel shake slightly when the lights went out, so he put his arm around her again.

After a few minutes of silence, without moving, Rachel whispered, "Tom?"

"Yes?" he whispered back.

Rachel was quiet a moment before she asked, "Will you tell me a story?"

Tom was surprised by this request, and he laughed quietly. "Sure," he said. "Do you want one of the bedtime storied I used to tell Ashley when she was little?"

Tom felt Rachel shake her head a little against his shoulder. "No," she whispered in the darkness. "Tell me our story."

Tom smiled, and thought about it for a while before he began. "Once upon a time, there was a Navy man who was the captain of a ship, and a beautiful scientist who was on a secret mission," he started.

"Paleomicrobiologist," Rachel whispered, and Tom laughed.

"Right. A beautiful paleomicrobiologist on a secret mission. The captain didn't know it at the time, but his ship was a part of her secret mission. As they sailed around the world, he slowly learned more and more about both the lady's mission, and the doctor herself." Tom paused, and looked down at the girl on his shoulder. In the darkness, he could just barely make out her smile. It warmed his heart. He couldn't believe how, after just a few short months together, this woman had taken such control over his life.

"The world was ending around them," Tom went on, "But the two were determined to save it. They fought many people Hell bent on stopping them from saving the world, and they lost people dear to both of them. Although they fought and bickered often, the two worked together closely, overcoming all the obstacles to their mission, and they were there for each other every step of the way." Tom paused, wondering if Rachel would recognize his words as the ones she had used in her letter. "And, after many challenges and a lot of hard work," he continued, "thanks to the doctor's brilliance, they saved the world." Tom smiled down at Rachel's head and added softly, "And though he didn't know it at the time, the captain was slowly falling in love with his beautiful scientist partner."

Tom trailed off, and after a lingering silence, Rachel whispered, "Tom?" He turned his head to look at her in the darkness, his eyes having adjusted so that he could now make out her face, but her eyes were still closed and her head was still resting on his shoulder. After a second, Rachel said, "I love you."

"I love you, too," Tom whispered back immediately, and hugged her tighter as she fell asleep. In that moment, Tom wanted nothing more than to stay sitting on that couch with her in his arms forever.


	5. Seeking Help

**A/N: I know it's been FOREVER since I got around to updating this story, so sorry about that! With the emotional roller coaster season 3 has been with regards to Rachel, I haven't really felt like writing. But I'm still not convinced she's gone, and I think what we all need right now is some good Tomchel fluff, so I wrote this addition. I already have an idea for the next chapter, so hopefully I won't keep you all waiting for weeks again lol. Anyway, sorry for the huge delay, and I hope you all like this chapter! Let me know what you think!**

The next day, Rachel had been called in to discuss the recent outbreaks of the virus with the President, and Tom had gone out to help get supplies to the ever increasing number of refugees pouring into St. Louis. He didn't get back to his hotel room until well after dinnertime, when most of the crew had already headed to bed, so as he hung his hat on the coatrack by his door, Tom was surprised when he heard a knock coming from the door that lead to Rachel's adjoining room.

Although surprised she was still awake, Tom smiled to himself when he heard the knock. "Yeah, Rach, come on in," he called.

On the other side of the door, Rachel smiled sheepishly to herself. She still wasn't completely used to his new nickname for her, but it made her ridiculously happy when he used it. Not that she'd admit that to him.

Tom watched as Rachel opened the door, and noticed with a frown that she had her medical bag in her hand. As soon as she walked in, Rachel saw Tom's eyes go straight to the med bag, and he looked back at her questioningly. Before she lost her nerve, Rachel asked, "Will you change my bandage?"

This only caused Tom's confused frown to deepen, and Rachel, embarrassed, blushed and hurriedly explained, "I know, it's ridiculous. I'm a doctor, and I've treated combat wounds before. I've dealt with worse wounds with your crew, even with you," she said. She could feel her cheeks getting hotter with embarrassment as she went along, so she quickly added, "I guess it's different trying to treat yourself."

To Rachel's relief, Tom finally smiled knowingly, and nodded. "You don't have to explain," he said, walking over to meet her in the doorway and take the medical bag from her hand. "I get it."

Rachel sighed with relief. She'd been so embarrassed about not being able to do it herself, and she was glad she hadn't had to go ask Rios to do it. Turns out these adjoining rooms were even more convenient that she'd thought.

Tom pulled a chair over to the small kitchen counter and gestured for her to sit up on the counter. He helped her climb up on the chair and up to the counter, and as Rachel sat down she found herself eye to eye with him. Tom gave her a reassuring smile, opened the medical bag, and began peeling off her old bandages.

"I don't know why I couldn't do it myself," Rachel said quietly, watching Tom's face as he concentrated on finding the right supplies in her bag. "It doesn't even hurt anymore…"

"It's okay," Tom said, trying to find a bandage that was the right size for her shoulder. As he sifted through the bag, he thought about how hard it must have been for Rachel to come ask for his help with this. Asking for help, especially with something that was completely within her domain as a doctor, went completely against her fiercely independent nature. Tom could tell she didn't like having to ask for help and was embarrassed, so she trying to justify and explain it. He was just thankful that, when faced with this crisis, it was him she had come to for help.

"Anything you need, things like this," Tom said, gesturing to her shoulder, "you know I'll be here for you, right? You don't have to worry about asking me," he said, finally finding the right bandage and meeting her eyes.

Rachel smiled at him, and some of the embarrassed color left her face. "I know," she said, and quietly added, "Thanks."

Tom nodded once and returned her smile before looking back to his work on her shoulder. He'd gotten the old bandage off, and was cleaning the wound with an antiseptic wipe. When he was done with that, he began wrapping the bandage around her shoulder. He heard Rachel make a quiet hiss of pain when the bandage got tight, and he muttered, "Sorry."

"It's okay," Rachel said through clenched teeth. "It's supposed to be tight. Perhaps," she added with an ironic laugh, "that's why I couldn't do it to myself."

Tom grinned at her sardonic humor and finished wrapping the bandage and securing it in place. "There," he said, "all done." Rachel watched as a satisfied smile filled his face and he ran his thumb over the top of her shoulder, avoiding the wounded area. He met her eyes briefly before leaning down and placing a gentle kiss on top of the bandage on her shoulder. "Feel better?" Tom whispered, looking back at her.

Rachel returned his smile, hers full of love, and whispered back, "much." Tom's smiled widened, and this time he leaned in and kissed Rachel's forehead, before she turned her head up and met his mouth with hers. Rachel sighed as Tom wrapped his warm arms around her waist, and she reached up with her good hand and ran it through his hair, pulling him closer and kissing him harder.

As soon as the two had lost themselves in each other, there was a knock on the door. Tom groaned and pulled away, and Rachel sighed in disappointment. Tom took a deep breath and tried to get a hold of himself, and when the knock sounded again, he gave Rachel an amused smile and a shrug that said, _I guess that's just our luck._ Rachel giggled and Tom shook his head, still grinning, and headed for the door.

Tom only opened the door a little, and he stood in the doorway, effectively blocking Rachel's view of their interrupter. She didn't have to wonder for long, however, because Tom said, "Lt. Burk." Rachel marveled at how much control he had over his voice already. He was back to the surly captain in an instant, and she was still stifling her laughs.

"Captain," Lt. Burk said. "Sorry to bother you so late, sir, but have you seen Dr. Scott?"

Tom was unsure what to say, and Rachel wasn't sure whether she wanted him to admit she was in his room at this hour or not. She had a feeling most of the crew already knew about them, but they hadn't really made anything official, and for now she wanted to keep it at rumors and speculation. She rather enjoyed the air of secrecy and privacy they had at the moment.

Tom was spared having to come up with a suitable response when Lt. Burk continued, "We knocked on her door, but she didn't answer. The President said he has some information on the shooter. He wants both of you in the conference room ASAP."

Tom nodded. "I'll find her," Tom said. "Tell the President we will be down as soon as we can."

"Yes sir," Burk said, and headed back down to deliver the message.

Tom turned back to Rachel, who sat open-mouthed on the counter where he'd left her. "Well," he said with a sigh, "looks like we have some more work to do."

Rachel just nodded absently, her mind whirring with possibilities, wondering what the President could want. Tom had said they caught the shooter, so what information could he have?

"Hey, Rachel," Tom said, bringing her back to the present. When her gaze once again focused on his, he asked, "You okay?"

"Yeah," Rachel said, taking Tom's offered arm and climbing back onto the chair to get off the counter. "Let's just get this over with."

Tom gave her a curt nod, retrieved his hat from the coatrack, and opened the door for her. She looked nervous as she headed out into the hallway. As Rachel passed him in the doorway, Tom stopped her with a light hand on her arm.

Rachel looked up at him, her eyes filled with a mix of confusion and worry. Tom knew she would rather just forget about the whole incident with the immune and move on, and he could see how she was dreading this meeting. "Whatever happens down there," he said quietly, "whatever information the President has, I'm here for you." Rachel just blinked at him, trying hard not to let her emotions get control of her. "You don't have to go through this alone," Tom whispered.

Some of the worry left Rachel's face, and she whispered back, "I know."


	6. Banishing Monsters

When Rachel walked into the conference room, the first thing she noticed was his face on the TV monitor, dominating most of the wall at the head of the U-shaped table. She froze in the doorway, shocked and frightened at being confronted with his face again. Thankfully, Tom was right behind her, and gave her arm a gentle squeeze, bringing her back to reality. Rachel shook her head, trying to dispel the image of his face from her mind, but that felt like a useless endeavor. She doubted she'd ever truly be rid of it.

Taking a deep breath to steady herself, Rachel entered the room, and Tom shut the door behind them. The noise of the closing door made the other three people in the room turn around. President Michener and Lts. Foster and Burk had been huddled close together, talking in low voices and occasionally motioning toward the portrait of Curtis, the rogue immune Rachel had identified as her would-be assassin.

Upon seeing that Tom and Rachel had arrived, President Michener broke away from the group and set a folder down on the edge of the table. "Dr. Scott, Commander Chandler, thank you for joining us," he said, giving them each a nod.

Rachel cast each of them wary looks before her gaze rested back on the picture of Curtis on the wall. "What is this about?" she asked, relieved when her voice came out steady. "I thought you caught him already…" Rachel tried to keep her eyes off the picture on the wall, but she was almost afraid to look away. Tom noticed how wary she looked, even though she was making sure to keep her face straight. The others likely missed how she kept glancing back at the picture and frowning, as if it were haunting her, but Tom didn't.

"We did," Michener assured her quickly. "But we have some more information about him that you need to know." He paused there, waiting for her confirmation before continuing.

Rachel looked from the President to the TV monitor and back, then nodded once. She wasn't sure she wanted to know anything about the man that still haunted her dreams. She'd rather just forget the entire incident and move on, but part of her wanted to know what the President had to say. Despite herself, she wanted to know what this man had against her, and what could have brought him to do what he did.

Tom stood to Rachel's side, watching her reactions. She looked scared, but also determined. Ready to face her fears, as always. Tom wished he could take her into his arms and reassure her that this monster was put away for good.

"As you know," Michener began, bringing Rachel's attention back to him, "he was one of the immunes. His name is Curtis." Rachel nodded. Tom had told her that much already. Michener continued, "He was McDowell's second in command, from what we can tell. We dug up as much as we could on him, but with the lack of news and media recently, there wasn't much. Fortunately," Michener smiled ruefully, "Tex was able to get him to talk."

Tom grinned at the thought of Tex interrogating Curtis until he gave up everything he knew, but Rachel remained stony-faced, still occasionally glancing at the picture on the wall.

"The good news is, he was acting on his own," Michener said. "After the downfall of the immunes, he took matters into his own hands."

"And came after me," Rachel said quietly, her voice a mixture of apprehension and disgust.

Michener nodded. "The bad news is, we don't know whether he told anyone else about his plans or not. He told Tex that there are still other immunes out there, and they'll 'carry on my work'."

"Meaning they could come after her again," Tom butted in, his voice laced with anger. He looked at Rachel for a reaction, but she was just staring at the President, her face blank. She had her emotions in tight check.

"Right," Michener said. "So for now, we're keeping you here in the hotel," he said to Rachel, "until we find out if there's anyone out there intent on finishing what Curtis started." Rachel winced a bit at that, but Michener had returned his attention to the file he had retrieved from the table, so he didn't notice. Tom did, though. "If you need to leave the hotel for any reason," Michener went on, "let both me and Commander Chandler know, and we'll give you an escort."

"So you're quarantining me?" Rachel protested indignantly, part of the worry on her face being replaced by annoyance. Tom smiled slightly to himself, glad he wasn't the one who had to tell her she was being quarantined.

"It's not permanent," Michener assured her. "Only until we are sure Curtis was working alone. It's for your own safety," he added lamely. Rachel rolled her eyes and sighed, but figured arguing was useless at this point. Taking the lack of protest as her consent, Michener closed his file and nodded. "Well, it's getting late, so unless there's anything else, I'll leave you to it. I assure you we're doing everything we can to assess the situation, but this seems to be the safest course of action at the moment."

Rachel, still annoyed but resigned to her fate, nodded. "I understand."

Michener returned her nod, and, gathering his things, headed out. Lt. Burk followed him out, nodding to both Tom and Rachel as he passed. Tom returned the nod, but Rachel was staring at the picture on the wall again, transfixed. Lt. Foster was the last to leave, giving Rachel a reassuring smile as she passed, but Rachel hardly noticed. Kara shot Tom a concerned look, but he simply nodded to her, telling her he'd take care of it. Kara had figured something was going on between Tom and Rachel since the night of the shooting, so she figured he could handle it, and left the two of them alone in the room, the imposing picture of Curtis still dominating the wall.

Tom walked over to Rachel's side, watching her face as she stared at the picture on the wall. Her look remained stoic, but he could tell she was simmering underneath. After a few moments he said, "Rachel."

She glanced at him, meeting his eyes briefly, but quickly turned back to the monitor. Tom moved in front of her, so he was standing between her and the screen, forcing her to meet his eyes. "Talk to me," he said quietly.

It was then that Rachel lost control. "Why?!" She demanded angrily, trying but failing to hold back angry tears. Embarrassed, she wiped at her eyes in frustration. "Why me? What… what would make someone do something like that?"

"I don't know," Tom said. "He's a monster, Rach."

Rachel wasn't listening. "Do you know what he said to me that night?" she demanded, and Tom shook his head, at a loss for how to console her. "'Sic semper tyrannis,'" Rachel spat angrily. "He called me a tyrant. A tyrant? All I wanted to do was save people," Rachel said, her anger mixing with sadness and frustration. "I don't understand," she said, "I just don't understand Tom…" Rachel tried to regain control of herself, but she was too far gone, and an angry sob escaped her lips.

Tom wrapped his arms around her, pulling her to him and hugging her tightly. He could feel her hot tears soaking through the fabric of his uniform. He stroked her hair and said, "we may never understand him, Rachel. He's a monster. What he did, it wasn't logical or rational. It doesn't make any sense. He did it out of blind hatred. You didn't deserve that, and you're no tyrant," he assured her quietly.

Rachel hugged him back tightly, seeking solace in his embrace. When her sobs started to subside and she regained some measure of control over her voice, she whispered, "I still have nightmares."

At that, Tom had to fight back angry tears of his own. He wanted to go down and put the fear of God into Curtis. He wanted to rob the monster of his happiness, the way he had robbed Rachel of hers. He wanted justice. He wanted Rachel to be able to sleep at night without fearing the man who had tried to take her life. He wanted Curtis dead.

But he also knew they needed him alive, for information. They needed to make sure Rachel was safe. That's why he had left the interrogation to Tex. Tom wasn't sure he could face the man and leave him in once piece.

Tom fought to control his own rage and kissed the top of Rachel's head, hugging her tighter. "I'll make sure nothing happens to you," he whispered back. "I'll keep you safe."

Rachel sniffled, burrowing her head into Tom's chest. "I know," she whispered. After a pause, she asked, "Tom?"

"Yeah?"

Rachel pulled back a bit so she could look up at him and asked, "Can I sleep in your room tonight?"

Despite everything, a small smile found its way to Tom's face. He wiped away a few tears that still clung to Rachel's cheek and said, "Of course." Meeting her eyes, he added, "And I'll make sure those nightmares don't come back."

Rachel returned his smile, then looked around him back to the monitor where Curtis' picture was still displayed. Tom let go of Rachel long enough to find the remote and switch the screen off, and Rachel sighed with relief. With the room left in near darkness, Tom took Rachel's hand and lead her back through the hotel to his room.

That night, Rachel slept curled up next to Tom, his arms wrapped around her protectively. As she fell asleep, Rachel thought about how far they had come in the last few days. Not long ago, Rachel wouldn't have admitted those feelings to anyone, not even Tom. It was hard for her to open up like that, to admit her feelings, but it was freeing, too. She had been alone for so long. For the first time in a long time, Rachel finally felt she had someone she could talk to. Someone to share her feelings, her fears, and her anger. She was glad they had talked, that night in Tom's hotel room. They were finally on the same page, and now, little by little, Rachel found herself able to trust Tom with her inner secrets. Being able to finally admit all of her fears and her anger, Rachel realized that she wasn't alone anymore, and that meant more to her than she would ever be able to explain. For the first time in a long time, Rachel realized, she didn't have to carry her burdens alone.

Rachel eventually drifted off to sleep, comforted by the thought that when she woke, Tom would still be there.

That night was the first night since she'd left the hospital that Curtis' face didn't haunt her dreams.


End file.
